So, I have this file with 1,314 sequences (file1) and another file with 566 sequences (file2). Each sequence has a proper barcode. What I can't understand is that in file1 the letters following the barcode are (number is count):
AAAGGGGCGCAGCAGGCGCG 1
AACGGGGCGACAGCAGGCGC 1
ACCGGGCGCAGCAGGCGCGA 1
ACGGGCGCAGCAGGCGCGAA 8
ACGGGCGCTAGCAGGCGCGA 1
ACGGGGACGCAGCAGGCGGA 1
ACGGGGCACAGCAGGCGCGA 1
ACGGGGCACAGTAGGCGCGA 1
ACGGGGCCAGCAGGCGCGAA 2
ACGGGGCCGCAGCAGGCGCG 2
ACGGGGCGAAAGCAGGCGCG 1
ACGGGGCGAGCAGGCGCGAA 1
ACGGGGCGCAAGCAGGCGCG 1
ACGGGGCGCACGCAGGCGCG 1
ACGGGGCGCAGCAAAGCGCG 1
ACGGGGCGCAGCAAGCGCGA 3
ACGGGGCGCAGCAAGGCGCG 3
ACGGGGCGCAGCACGCGCGA 1
ACGGGGCGCAGCACGGCGCC 1
ACGGGGCGCAGCACGGCGCG 3
ACGGGGCGCAGCACGGCGGC 4
ACGGGGCGCAGCAGACGCGA 4
ACGGGGCGCAGCAGGAGCGA 1
ACGGGGCGCAGCAGGCACGA 3
ACGGGGCGCAGCAGGCGACG 5
ACGGGGCGCAGCAGGCGCCG 1
ACGGGGCGCAGCAGGCGCGA 1219
ACGGGGCGCAGCAGGCGGCG 2
ACGGGGCGCAGCAGGCTCGA 1
ACGGGGCGCAGCATGCGCGA 1
ACGGGGCGCAGCTACGGCGC 3
ACGGGGCGCAGGCAGGCGCG 1
ACGGGGCGCAGTAGGCGCGA 1
ACGGGGCGCAGTCACGGCGC 1
ACGGGGCGCAGTCAGGCCGC 1
ACGGGGCGCAGTCAGGCGCG 5
ACGGGGCGCCGCAGGCGCGA 3
ACGGGGCGCGCAGGCGCGAA 1
ACGGGGCGCTAGTCAGGCGC 2
ACGGGGCGGCAGCAGGCGCG 3
ACGGGGGCGCAGCAGGCGCG 13
ACGGGGGGCGCAGCAGGCGC 1
ACGGGTCGCAGCAGCGCGAA 1
AGTGGGGCGCAGCAGGCGCG 1
ATGGGGCGCAGCAGGCGCGA 1
GACGGGGCGCAGCAGGCGAC 3
GACGGGGCGCAGCAGGCGCG 2
However, in file2:
AACGGGGCGTCAGCAGGGCG 1
ACGGGCCGCAGCAGGGCGCG 1
ACGGGCGCAGCAGGCGCGAA 2
ACGGGCGCAGCAGGGCGCGA 151
ACGGGCGCTAGCACGGCGGC 1
ACGGGCGCTAGCACGGGCGG 1
ACGGGCGCTAGCAGGCGCGA 1
ACGGGCGCTAGCAGGCGCGG 2
ACGGGCGCTAGCAGGGCGCG 1
ACGGGCGCTAGCAGGGCGGC 1
ACGGGCGGCAGCAGGGCGCG 1
ACGGGCGTCAGCAGGACGCG 1
ACGGGCGTCAGCAGGCGGCG 3
ACGGGCGTCAGCAGGGCGCG 3
ACGGGCGTCAGCAGGGCGGC 1
ACGGGCGTCAGCAGGGGCGC 1
ACGGGGCCAGCAGGGCGCGA 3
ACGGGGCCGCAGCAGGGCGC 2
ACGGGGCGAAGCAGGGCGCG 1
ACGGGGCGAGCAGGGCGCGA 1
ACGGGGCGCAGCAAGCGCGA 1
ACGGGGCGCAGCAGCGCGAA 1
ACGGGGCGCAGCAGGGCGAC 2
ACGGGGCGCAGCAGGGCGCG 340
ACGGGGCGCAGCAGGGCGGC 8
ACGGGGCGCAGCAGGGGCGC 1
ACGGGGCGCAGCAGGGTGCG 4
ACGGGGCGCAGCAGTCGCGA 1
ACGGGGCGCTAGCAGGGCGC 1
ACGGGGCGCTAGCAGGGCGG 1
ACGGGGCGTCAGCAGGGCGC 4
ACGGGGCGTCAGCAGGGCGG 4
ACGGGGCGTCAGCAGGGGCG 5
ACGGGGCGTCAGCTAGGGGC 1
ACGGGGCTAGCAGGCGCGGA 1
ACGGGGTCGCAGCAGGGCGC 5
ACGGGGTCGCAGCAGGGGCG 3
ACGGGTCGCAGCAGGGCGCG 1
ACGGGTGCAGCAGGGCGCGA 1
ACGGGTGTCAGCAGGGCGCG 1
ATGGGGGCGCAGCAGGGCGC 1
CCGGGGCGCAGCAGGGCGCG 1
GACGGGCGCAGCAGGGCGCG 1
GACGGGGCGCAGCAGGGCGA 1
GACGGGGCGCAGCAGGGCGC 1
The same forward primer 'ACGGGGCGCAGCAGGCGCGA' (the most abundant seq in file1) was used for both files. It's not even present in file2. How can this be? It's as if file2 is barcoded but the primer has been removed or something?
-
Barcoded files, a lot of variance in supposed primers, help me understand
Last edited by rhinoceros; 10-17-2013, 05:22 AM.
-
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...08-27-2024, 04:44 AM -
Sequencing mRNA provides a snapshot of cellular activity, allowing researchers to study the dynamics of cellular processes, compare gene expression across different tissue types, and gain insights into the mechanisms of complex diseases. “mRNA’s central role in the dogma of molecular biology makes it a logical and relevant focus for transcriptomic studies,” stated Sebastian Aguilar Pierlé, Ph.D., Application Development Lead at Inorevia. “One of the major hurdles for...08-07-2024, 12:11 PM